THE HYBRID HISTORY OF ZEBRAFISH

Abstract

Since the description of the zebrafish Danio rerio in 1822, the identity of its closest living relative has been unclear. To address this problem, we sequenced the exomes of ten species in genus Danio and used them to infer relationships across the 25 chromosomes of the zebrafish genome. The majority of relationships within Danio were remarkably consistent across all chromosomes. Relationships of chromosome segments, however, depended systematically upon genomic location within zebrafish chromosomes. Regions near chromosome centers identified D. kyathit and/or D. aesculapii as the closest relative of zebrafish, while segments near chromosome ends supported only D. aesculapii as the zebrafish sister species. Genome-wide comparisons of derived character states revealed that danio relationships are inconsistent with a simple bifurcating species history and support an ancient hybrid origin of the D. rerio lineage. We also found evidence of more recent gene flow limited to the high recombination ends of chromosomes and several megabases of chromosome 20 with a history distinct from the rest of the genome. The additional insight gained from incorporating genome structure into a phylogenomic study demonstrates the utility of such an approach for future studies in other taxa. The multiple genomic histories of species in the genus Danio have important implications for comparative studies in these species and for our understanding of the hybrid evolutionary history of zebrafish.